6B7J | pdb_00006b7j

The crystal structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Vibrio cholerae O1 biovar eltor str. N16961

• PDB DOI: https://doi.org/10.2210/pdb6B7J/pdb

• Classification: LYASE
• Organism(s): Vibrio cholerae O395
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2017-10-04 Released: 2017-11-01 
• Deposition Author(s): Tan, K., Gu, M., Nocek, B., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.158 (Depositor) 

Starting Model: experimental

Literature

The crystal structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Vibrio cholerae O1 biovar eltor str. N16961

Tan, K., Gu, M., Nocek, B., Joachimiak, A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 38.76 kDa 
• Atom Count: 3,088 
• Modeled Residue Count: 347 
• Deposited Residue Count: 350 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase	A, B	175	Vibrio cholerae O395	Mutation(s): 0  Gene Names: fabA, VC0395_A1091, VC395_1603 EC: 4.2.1.59 (PDB Primary Data), 5.3.3.14 (PDB Primary Data)
UniProt
Find proteins for A5F850 (Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395)) Explore A5F850  Go to UniProtKB:  A5F850

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	C [auth A], D [auth B]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.194 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.156 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.158 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.52	α = 90
b = 85.263	β = 97.11
c = 49.932	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-11-01 
Deposition Author(s): Tan, K., Gu, M., Nocek, B., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2017-11-01
  Type: Initial release
  
• Version 1.1: 2017-12-06
  Changes: Author supporting evidence
• Version 1.2: 2022-03-23
  Changes: Advisory, Author supporting evidence, Database references
• Version 1.3: 2023-10-04
  Changes: Data collection, Refinement description